Lawyers for former AFL player and alleged rapist Stephen Milne have accused Victoria Police of running a "bizarre" public relations exercise over its handling of the case.

The former St Kilda forward is facing four counts of rape over allegations he sexually assaulted a 19-year-old woman at the home of former teammate Leigh Montagna in 2004.

An original investigation by police in 2004 did not result in charges, but when two former detectives alleged the case was mishandled, the now defunct Office of Police Integrity (OPI) launched an investigation.

Lawyers for the Chief Commissioner told the court that an investigation into the police handling of the matter in 2004 is still ongoing before the Independent Broad-based Anti-corruption Commission (IBAC), which replaced the OPI.

The court heard some material requested by Milne's lawyers will be subject to a public indemnity claim because it needs to remain confidential.

Defence lawyer Philip Dunn SC accused the top command in Victoria Police of running a public image campaign to place police in better light.

He said Victoria Police had tried to gain advantage by making out police are "the good guys".

Mr Dunn said Chief Commissioner Ken Lay and the Assistant Commissioner Steve Fontana gave radio interviews about the original police investigation, but now want some information to remain secret.

"Smells like police selectively release things and hide other things," he told the court.

He said police now will not say who "is rotten in the barrel".

The court heard IBAC has provided some information to the complainant.

An OPI report released in 2010 found there was no miscarriage of justice by police handling the original case.

The court heard some evidence has gone missing since 2004, including phone records and text messages sent by the complainant to Milne, Montagne and her friend, and original witness statements.